Publications of Yufeng Liu

 

·      Hu, Y., Huang, Y.,  Du, Y., Orellana, C., Singh, D., Kuan, P., Scott, R., Scott, H., Chiang, D., Hayes, N., Jones, C.,  Liu, Y.,  Prins, J., and Liu, J.  DiffSplice: the Genome-Wide Detection of Differential Splicing Events with RNA-seq.  Nucleic Acids Research, to appear.

·      Lee, W., Du., Y., Sun, W., Hayes, D. N., and Liu, Y. Multiple response regression for Gaussian mixture models with known labels. Statistical Analysis and Data Mining, to appear.

·      Huang, H., Liu, Y., and Marron, J. S. Bi-directional discrimination with application to data visualization. Biometrika, to appear.

·      The Cancer Genome Atlas Research Network. Comprehensive genomic characterization of squamous cell lung cancers. Nature, to appear.

·      Huang, H., Liu, Y., Du, Y., Perou, C., Hayes, D. N., Todd, M., and Marron, J. S. Multiclass distance weighted discrimination.  Journal of Computational and Graphical Statistics, to appear.

·      Wang, P., Dong, Q., Zhang. C., Kuan. P.F., Liu, Y., Jeck, W.R., Andersen, J.B., Jiang W, Savich GL, Tan TX, Auman JT, Hoskins JM, Misher AD, Yourstone YM, Kim JW, Cibulskis K, Getz G, Hunt HV, Thorgeirsson SS, Roberts LR, Ye D, Guan KL, Xiong Y, Qin LX, Chiang DY.  Mutations in isocitrate dehydrogenase 1 and 2 occur frequently in intrahepatic cholangiocarcinomas and share hypermethylation targets with glioblastomas. Oncogene, to appear.

·      Wu, Y. and Liu, Y. Adaptively weighted large margin classifiers. Journal of Computational and Graphical Statistics, to appear.

·      Wu, Y. and  Liu, Y.  Functional robust support vector machines for sparse and irregular longitudinal data. Journal of Computational and Graphical Statistics, to appear.

·      Huang, H., Lu, X., Liu, Y., Haaland, P., and Marron, J. S. (2012). R/DWD: Distance weighted discrimination for classification, visualization and batch adjustment. Bioinformatics, 28, 8, 1182-1183.

·      Lee, W. and Liu, Y. (2012). Simultaneous multiple response regression and inverse covariance matrix estimation via penalized Gaussian maximum likelihood. Journal of Multivariate Analysis, 111, 241-255.

·      Huang, Y., Hu, Y., Jones, C. D., MacLeod, J. N., Chiang, D. Y., Liu, Y., Prins, J. F., and Liu, J. (2012). A robust method for transcript quantification with RNA-seq data. Research in Computational Molecular Biology (RECOMB), Lecture Notes in Computer Science, 7262,127-147.

·      Zhang, H. H., Cheng, G. and Liu, Y. (2011). Linear or Nonlinear? Automatic Structure Discovery for Partially Linear Models. Journal of the American Statistical Association, 106, 495, 1099-1112.

·      Liu, Y. and Yuan, M. (2011). Reinforced multicategory support vector machines. Journal of Computational and Graphical Statistics, 20, 4, 901–919.

·      Samarov, D., Marron, J.S., Liu, Y., Grulke, C., and Tropsha, A. (2011). Local kernel canonical correlation analysis with application to virtual drug screening. Annals of Applied Statistics, 5, 3, 2169-2196.

·      Singh D., Orellana C., Hu Y., Jones C. D., Liu Y., Chiang D., Liu J., Prins J. F. (2011). FDM: A Graph-based Statistical Method to Analyze Differential Transcription using RNA-seq data. Bioinformatics, 27, 2633-2640.

·      Liu, Y., Zhang, H. H., and Wu, Y. (2011). Soft or hard classification? Large margin unified machines. Journal of the American Statistical Association, 106, 166-177.

·      Liu, Y. and Wu, Y. (2011). Simultaneous multiple non-crossing quantile regression estimation using kernel constraints. Journal of Nonparametric Statistics, 23, 2, 415-437.

·      Ang, M. K., Patel, M. R.,  Yin, X. Y.,  Fritchie, K.,  Zhao, N., Liu, Y., Wilkerson, M.,  Weissler, M. C.,  Shockley, W.,  Couch,  M. E., Zanation, A. M.,   Hackman, T.,  Chera, B.,   Harris,  S. L.,  Miller,  C. R., Thorne,  L. B., Hayward, M. C.,  Funkhouser, W. K.,  Olshan, A. F.,  Shores, C. G., and Hayes, D. N. (2011). High XRCC1 expression is associated with poorer survival in patients with head and neck squamous cell carcinoma. Clinical Cancer Research, 17, 20, 6542-6552.

·      Fan, C., Prat, A., Parker, J., Liu, Y., Carey, L., Troester, M., and Perou, C. (2011). Building prognostic models for breast cancer patients using clinical variables and hundreds of gene expression signatures. BMC Medical Genomics, 4:3, 1-15.

·      Park, S. Y. and Liu, Y. (2011). Robust penalized logistic regression with truncated loss. The Canadian Journal of Statistics, 39, 2, 300-323.

·      Wu, Y. and Liu, Y. (2011). Non-crossing large-margin probability estimation and its application to robust SVM via preconditioning. Statistical Methodology, 8, 56-67.

·      Qiao, X., Zhang, H. H., Liu, Y., Todd, M. J., and Marron, J. S. (2010). Weighted distance weighted discrimination and its asymptotic properties. Journal of the American Statistical Association, 105, 489, 401-414.

·      Park, S. Y., Liu, Y., Liu, D., and Scholl, P. (2010).  Multicategory composite least-squares classifiers. Statistical Analysis and Data Mining, 3, 4, 272-286.

·      Wu, Y., Zhang, H. H., and Liu, Y. (2010). Robust Model-free Multiclass Probability Estimation. Journal of the American Statistical Association, 105, 489, 424-436.

·      Wilkerson, M. D.,  Yin, X.,  Hoadley, K. A.,  Liu, Y., Hayward, M. C.,  Miller, C. R.,  Randell, S. H.,  Socinksi, M.,  Parsons, A. M.,  Funkhouser, W. K., Lee, C.,  Roberts, P.,   Thorne, L.,  Bernard, P. S., Perou, C. M.,  and Hayes, D. N. (2010). Lung squamous cell carcinoma mRNA expression subtypes are reproducible, clinically-important and correspond to different normal cell types. Clinical Cancer Research, 16, 4864-4875.

·      Liu, Y., Wu, Y., and He, Q. (2010). Utility-based weighted multicategory robust Support Vector Machines. Statistics and Its Interface, 3, 465-476.

·      Zhu, Z. and Liu, Y. (2009). Estimating spatial covariance using penalized likelihood with weighted L1 penalty. Journal of Nonparametric Statistics, 21, 7, 925-942.

·      Qiao, X. and Liu, Y. (2009). Adaptive weighted learning for unbalanced multicategory classification. Biometrics, 65, 159-168.

·      Wu, Y. and Liu, Y. (2009). Stepwise multiple quantile regression estimation using non-crossing constraints. Statistics and Its Interface, 2, 299-310.

·      Park, S. Y. and Liu, Y. (2009). From the support vector machine to the bounded constraint machine. Statistics and Its Interface, 2, 285-298.

·      Wu, Y. and Liu, Y. (2009). Variable selection in quantile regression. Statistica Sinica, 19, 801-817.

·      Liu, Y., Hayes, D. N., Nobel, A., and Marron, J. S. (2008). Statistical significance of clustering for high dimension low sample size data. Journal of the American Statistical Association, 103, 483, 1281-1293.

·      Zhang, H. H., Liu, Y.,  Wu, Y., and Zhu, J. (2008). Variable selection for the multicategory SVM via sup-norm regularization. Electronic Journal of Statistics, 2, 149-167.

·      Liu, Y. (2008). Discussion of “Sure independence screening for ultrahigh dimensional feature space” by Fan and Lv, Journal of Royal Statistical Society, Series B, 70, 898-899.

·      Wang, J., Shen, X., and Liu, Y. (2008). Probability estimation for large margin classifiers. Biometrika, 95, 1, 149-167.

·      Liu, Y. (2007). Fisher consistency of multicategory support vector machines. Eleventh International Conference on Artificial Intelligence and Statistics, 289-296.

·      Liu, Y. and Wu, Y. (2007). Variable selection via a combination of the L0 and L1 penalties. Journal of Computational and Graphical Statistics, 16, 4, 782-798.

·      Wu, Y. and Liu, Y. (2007). Robust truncated-hinge-loss support vector machines. Journal of the American Statistical Association, 102, 479, 974-983.

·      Li, Y., Liu, Y., and Zhu, J. (2007). Quantile regression in Reproducing Kernel Hilbert Spaces. Journal of the American Statistical Association, 102, 477, 255-268.

·      Liu, Y., Ruan, S., and Dean, A. M. (2007). Construction and analysis of Es­2 efficient supersaturated designs. Journal of Statistical Planning and Inference, 137, 5,1516-1529.

·      Liu, Y., Zhang, H. H., Park, C., and Ahn, J. (2007). Support Vector Machines with adaptive Lq penalties. Computational Statistics and Data Analysis, 51, 12, 6380-6394.

·      Alcorta, D., Barnes, D. A.,  Dooley, M. A., Sullivan, P., Jonas, B., Liu, Y., Lionaki, S., Reddy, C. B., Chin, H., Dempsey, A. A., Jennette, J. C., and Falk, R. J. (2007). Leukocyte Gene Expression Signatures in Antineutrophil Cytoplasmic Autoantibody (ANCA) and Lupus Glomerulonephritis, Kidney International, 72, 853-864.

·      Liu, Y. and Wu, Y. (2006). Optimizing psi-learning via mixed integer programming. Statistica Sinica, 16, 2, 441-457.

·      Liu, Y. and Shen, X. (2006). Multicategory psi-learning. Journal of the American Statistical Association, 101, 474, 500-509.

·      Liu, Y., Shen, X., and Doss, H. (2005). Multicategory psi-learning and support vector machine: computational tools. Journal of Computational and Graphical Statistics, 14, 1, 219-236.

·      Liu, Y. and Dean, A. M. (2004). k-circulant supersaturated designs. Technometrics, 46, 1, 32-43.